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<h2>Alignment & Synteny Parameters</h2>

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These parameters apply to the alignment, anchor filtering/loading, 
and synteny computation for a pair of projects. 
<p>
If you want to re-use parameters from a previous pair, first close
the Parameters window, then select the project
pair in the "Available Syntenies" table, and then re-open
the Parameters window and use the "Load Previous" button. 
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<p>
<table border='1' cellpadding='5' rules=all >
<tr>
	<td align="left">
		<b>Parameter</b>
	</td>
	<td align="left" >
		<b>Description</b>
	</td>
	<td align="left" >
		<b>Stage</b>
	</td>
	<td align="left">
		<b>Default Value</b>
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Top N
	</td>
	<td align="left"  valign="top" width="350" >
		Retain the top N hits for every sequence region (as 
		well as all hits with score at least 80% of the Nth). 
	</td>
	<td align="left"  valign="top" >
		Anchor Load
	</td>	
	<td align="left"  valign="top" >
		2
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Min Dots
	</td>
	<td align="left"  valign="top" width="350" >
		Minimum number of anchors required to define
		a synteny block.
	</td>
	<td align="left"  valign="top" >
		Synteny
	</td>
	<td align="left"  valign="top" >
		7
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		Merge Blocks
	</td>
	<td align="left"  valign="top" width="350" >
		Merge overlapping (or nearby) synteny blocks into larger
		blocks. 
	</td>
	<td align="left"  valign="top" >
		Synteny
	</td>	
	<td align="left"  valign="top" >
		Off
	</td>
</tr>
<!--tr>
	<td align="left" valign="top">
		Do Synteny
	</td>
	<td align="left"  valign="top" width="350" >
		Carry out the synteny block computation.
	</td>
	<td align="left"  valign="top" >
		Synteny
	</td>	
	<td align="left"  valign="top" >
		On
	</td>
</tr-->
<tr>
	<td align="left" valign="top">
		No Overlapping Blocks
	</td>
	<td align="left"  valign="top" width="350" >
		If two synteny blocks overlap on a chromosome, keep only
		the larger one.
	</td>
	<td align="left"  valign="top" >
		Synteny
	</td>	
	<td align="left"  valign="top" >
		Off
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		NUCmer Only
	</td>
	<td align="left"  valign="top" width="350" >
		User NUCmer for all alignments.*
	</td>
	<td align="left"  valign="top" >
		Align
	</td>
	<td align="left"  valign="top" >
		Off
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		PROmer Only
	</td>
	<td align="left"  valign="top" width="350" >
		User PROmer for all alignments.*
	</td>
	<td align="left"  valign="top" >
		Align
	</td>
	<td align="left"  valign="top" >
		Off
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		BLAT Args
	</td>
	<td align="left"  valign="top" width="350" >
		Arguments for BLAT (FPC alignments only)
	</td>
	<td align="left"  valign="top" >
		Align
	</td>
	<td align="left"  valign="top" width="250" >
		-minScore=30 -minIdentity=70 -tileSize=10 -qMask=lower -maxIntron=10000
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		NUCmer Args
	</td>
	<td align="left"  valign="top" width="350" >
		Arguments for NUCmer
	</td>
	<td align="left"  valign="top" >
		Align
	</td>
	<td align="left"  valign="top" width="250" >
		&nbsp;
	</td>
</tr>
<tr>
	<td align="left" valign="top">
		PROmer Args
	</td>
	<td align="left"  valign="top" width="350" >
		Arguments for PROmer
	</td>
	<td align="left"  valign="top" >
		Align
	</td>
	<td align="left"  valign="top" width="250" >
		&nbsp;
	</td>
</tr>
</table>
<p>
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* Note that, by default, PROmer is used for alignments between different
projects, while NUCmer is used for self alignments.
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